Unveiling the molecular architecture of T cells and immune synapses with cryo-expansion microscopy

Florent Lemaître; Olivier Mercey; Isabelle Mean; Elise Paulin; Valérie Dutoit; Jan A Rath; Christine von Gunten; Denis Migliorini; Caroline Arber; Paul Guichard; Virginie Hamel; Benita Wolf

doi:10.1016/j.celrep.2026.117165

Unveiling the molecular architecture of T cells and immune synapses with cryo-expansion microscopy

Cell Rep. 2026 Apr 1;45(4):117165. doi: 10.1016/j.celrep.2026.117165. Online ahead of print.

Authors

Affiliations

¹ Department of Molecular and Cellular Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland.
² Brain Tumor and Immune Cell Engineering Laboratory, Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Swiss Cancer Center Léman, Lausanne, Switzerland; Agora Cancer Research Center, Lausanne, Switzerland.
³ Swiss Cancer Center Léman, Lausanne, Switzerland; Agora Cancer Research Center, Lausanne, Switzerland; Department of Oncology UNIL-CHUV, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland; Ludwig Institute for Cancer Research Lausanne Branch, Lausanne, Switzerland.
⁴ Department of Oncology UNIL-CHUV, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland; Ludwig Institute for Cancer Research Lausanne Branch, Lausanne, Switzerland.
⁵ Brain Tumor and Immune Cell Engineering Laboratory, Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Department of Oncology, University Hospital of Geneva, Geneva, Switzerland; Swiss Cancer Center Léman, Lausanne, Switzerland; Agora Cancer Research Center, Lausanne, Switzerland.
⁶ Swiss Cancer Center Léman, Lausanne, Switzerland; Agora Cancer Research Center, Lausanne, Switzerland; Department of Oncology UNIL-CHUV, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland; Ludwig Institute for Cancer Research Lausanne Branch, Lausanne, Switzerland; Service of Immuno-Oncology, Department of Oncology UNIL-CHUV, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland; Service of Hematology and Central Laboratory of Hematology, Department of Oncology UNIL-CHUV and, Departments of Oncology, Laboratory Medicine and Pathology, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland.
⁷ Department of Molecular and Cellular Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland. Electronic address: virginie.hamel@unige.ch.
⁸ Department of Molecular and Cellular Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland; Swiss Cancer Center Léman, Lausanne, Switzerland; Agora Cancer Research Center, Lausanne, Switzerland; Department of Oncology UNIL-CHUV, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland. Electronic address: benita.wolf@chuv.ch.

PMID: 41926287
DOI: 10.1016/j.celrep.2026.117165

Abstract

Cytotoxic T cell killing is executed at the immunological synapse, whose nanoscale organization underlies function but remains difficult to resolve in native states. Here, we apply cryo-expansion microscopy (cryo-ExM) to visualize the near-native three-dimensional architecture of human T cell synapses and cytotoxic organelles. Cryo-ExM preserves actin, microtubules, membranes, and fine membrane protrusions with high fidelity, enabling volumetric quantification of synapse morphogenesis. We identify an adhesion-dependent, dome-like membrane architecture beneath activated T cells that collapses upon ICAM-1 engagement, linking synapse topology to adhesive cues. Cryo-ExM further resolves intact lytic granules in primary human CD4 and CD8 T cells, revealing single-core and multi-core ultrastructures, spatial organization, and perforin and granzyme loading. Using tissue-adapted expansion microscopy, we map cytotoxic granule content in tumor-infiltrating T cells in FFPE human brain tumors. Together, these data establish a near-native structural framework for human T cell cytotoxicity and an imaging workflow bridging cell models and clinical tissues.

Keywords: 3D ultrastructure; CP: immunology; T cell cytotoxicity; cryo-expansion microscopy; cytotoxic granule deployment; immune synapse; lytic granules; tumor-infiltrating lymphocytes.